Why your Microbiome Might be the Source of your Digestive Problems

When it comes to battling issues like acid reflux, it’s important to listen to your gut.

By Melissa Jacobs

​Heartburn, acid reflux, gastroesophageal reflux disease. Whatever name it goes by, the digestive disorder affects millions of Americans, making antacids a billion-dollar business. According to Statista, an online statistics company, $859.6 million worth of store-brand generic antacids were sold in 2016. Nexium 24HR, Prilosec OTC and Zantac 150 had combined sales of $689.7 million, and prescription drugs were sold for millions more.

GERD is only one of many ailments and allergies that create tummy troubles. Irritable bowel syndrome, Crohn’s, celiac disease, lactose intolerance and other conditions are so common that they are reaching almost epidemic levels. What’s causing so much havoc? “When in doubt, look in the gut,” says Dr. Rashna Staid, an integrative medicine specialist at Jefferson Health’s Marcus Institute of Integrative Health in Villanova.

Staid focuses on addressing disorders created by microbiome, the trillions of microscopic genomes that live in bodies, especially in our guts. Discovered via the Human Genome Project, microbiome are nonhuman organisms—bacteria, fungi, viruses, etc.—deposited into bodies by eating, drinking, breathing and living life on Earth.

But microbiome are not disease-carrying harbingers of evil. Modern-minded physicians like Staid, who’s board certified in internal medicine, believe that we actually need more microbiome. “One common problem is that microbiome diversity is very low,” she says. “That means the bacteria in your gut is more like Iowa than New York City. To make our bodies run correctly, we need diverse, healthy microbiome. The linings of our guts exist to allow in what needs to get in and keep out what doesn’t. But the permeability of those linings has changed because of what we put into our bodies.”

Dr. Darwin Deen agrees. A Western-trained family physician with extensive training in Eastern-based functional medicine, restorative medicine and nutrition, Deen practices at the Yang Institute of Integrative Medicine in Bryn Mawr. “Chronic conditions like those involving the GI tract are often manifestations of accumulated insults from a variety of areas,” Deen says.

Those insults can vary from overusing antibiotics to eating canned foods. “Most people are not on diets that support healthy microbiome,” Deen says. “If you eat processed foods, even if they are vegetables, you’re not getting farm-grown food and the good bacteria that comes with it. A lot of bacteria are important to our bodies. We get rid of them at our peril.”

Are microbiome really that powerful? Don’t genetics play a big role in predisposing people to GERD, IBS and other diseases? “Yes, but genetics are only the blueprint,” Staid says. “Your health depends on the building materials. If you use crappy materials, you get crappy results—even with great blueprints.”

Probiotics and elimination diets are popular ways to attempt to reset a gut’s microbiome. But Staid and Deen agree that those are Band-Aid approaches, doomed to fail. “Microbiome changes slowly over time, but the whole body needs to support those changes to make them last,” Deen says. “And they have to be the right changes. Are you eliminating and ingesting the right things for your particular system?”

From weight-loss plans to dairy-free, gluten-free regimens, too many diets don’t take into consideration the GI-unfriendly toxins that are embedded in food. For example, the Paleo and Atkins diets prescribe low carbohydrates and high proteins—but what kind of proteins? “If you’re eating meat from a cow that was fed corn, you are eating that corn, which was sprayed with pesticides,” Staid says. “Truth is, cows normally eat grass, so they aren’t properly digesting corn and grains. That cow likely got antibiotics, which you are also getting.”

Eating organic meat, fruits and vegetables is always better, but even that’s too simplistic, the physicians say. “For example, people eat salad because they think it is healthy, but it is actually more difficult for the body to process raw food than cooked food,” Deen says.

What are the right things to eat? It depends on the person, the doctors agree. People suffering with chronic GI issues need full evaluations, starting with testing their microbiomes through stool samples. The doctors also do bloodwork to test for vitamins and mineral deficiencies. This personalized precision medicine carries a hefty price tag. Health insurance covers little or none of the tests or doctors’ fees.

But the tests do reveal underlying nutritional and microbiome problems. Deficiencies in vitamins D and B12, magnesium and iron are the most common results. Using that information, the doctors create food plans for their patients. Sticking to those diets can be tough, but compliance isn’t mandatory forever. “Once we fix the microbiome, we heal the inflammation,” Staid says. “It’s like a glass overflowing its edges—if I can get you down to halfway, you won’t overflow if you have a little water. But in crisis, we have to turn off the faucet.”